Starting phenix.real_space_refine
on Wed Mar  5 23:48:08 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8bgv_16039/03_2025/8bgv_16039.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bgv_16039/03_2025/8bgv_16039.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.27
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8bgv_16039/03_2025/8bgv_16039.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bgv_16039/03_2025/8bgv_16039.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bgv_16039/03_2025/8bgv_16039.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bgv_16039/03_2025/8bgv_16039.cif"
  }
  resolution = 3.27
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       7      5.16       5
     C    2569      2.51       5
     N     756      2.21       5
     O     777      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4109
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 587
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
  Restraints were copied for chains:
    C, B, E, D, F, n
  Time building chain proxies: 2.27, per 1000 atoms: 0.55
  Number of scatterers: 4109
  At special positions: 0
  Unit cell: (145.95, 100.08, 40.032, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       7     16.00
     O     777      8.00
     N     756      7.00
     C    2569      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.85
  Conformation dependent library (CDL) restraints added in 473.8 milliseconds
  

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  938

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 16 sheets defined
      0.0% alpha, 24.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.57
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 305 through 310
      removed outlier: 6.670A  pdb=" N   SER n 305 " --> pdb=" O   VAL B 306 " (cutoff:3.500A)
      removed outlier: 8.442A  pdb=" N   ILE B 308 " --> pdb=" O   SER n 305 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   GLN n 307 " --> pdb=" O   ILE B 308 " (cutoff:3.500A)
      removed outlier: 8.036A  pdb=" N   TYR B 310 " --> pdb=" O   GLN n 307 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   VAL n 309 " --> pdb=" O   TYR B 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314
      removed outlier: 6.784A  pdb=" N   VAL n 313 " --> pdb=" O   ASP B 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 318
      removed outlier: 6.351A  pdb=" N   LYS n 317 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330
      removed outlier: 6.405A  pdb=" N   HIS n 329 " --> pdb=" O   HIS B 330 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 346 through 348
      removed outlier: 5.716A  pdb=" N   LYS A 347 " --> pdb=" O   ASP B 348 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   LYS B 347 " --> pdb=" O   PHE n 346 " (cutoff:3.500A)
      removed outlier: 5.716A  pdb=" N   LYS n 347 " --> pdb=" O   ASP E 348 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 351 through 352
      removed outlier: 6.700A  pdb=" N   GLN n 351 " --> pdb=" O   SER B 352 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 369 through 373
      removed outlier: 6.121A  pdb=" N   LYS A 370 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
      removed outlier: 7.744A  pdb=" N   THR B 373 " --> pdb=" O   LYS A 370 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   GLU A 372 " --> pdb=" O   THR B 373 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   LYS n 370 " --> pdb=" O   ILE E 371 " (cutoff:3.500A)
      removed outlier: 7.745A  pdb=" N   THR E 373 " --> pdb=" O   LYS n 370 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   GLU n 372 " --> pdb=" O   THR E 373 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 376 through 379
      removed outlier: 6.586A  pdb=" N   LEU A 376 " --> pdb=" O   THR B 377 " (cutoff:3.500A)
      removed outlier: 8.404A  pdb=" N   ARG B 379 " --> pdb=" O   LEU A 376 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   PHE A 378 " --> pdb=" O   ARG B 379 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   LEU n 376 " --> pdb=" O   THR E 377 " (cutoff:3.500A)
      removed outlier: 8.405A  pdb=" N   ARG E 379 " --> pdb=" O   LEU n 376 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   PHE n 378 " --> pdb=" O   ARG E 379 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 305 through 310
    Processing sheet with id=AB1, first strand: chain 'C' and resid 313 through 314
    Processing sheet with id=AB2, first strand: chain 'C' and resid 317 through 318
    Processing sheet with id=AB3, first strand: chain 'C' and resid 328 through 330
    Processing sheet with id=AB4, first strand: chain 'C' and resid 346 through 348
      removed outlier: 5.716A  pdb=" N   LYS C 347 " --> pdb=" O   ASP D 348 " (cutoff:3.500A)
      removed outlier: 5.716A  pdb=" N   LYS D 347 " --> pdb=" O   ASP F 348 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'C' and resid 351 through 352
    Processing sheet with id=AB6, first strand: chain 'C' and resid 369 through 373
      removed outlier: 6.121A  pdb=" N   LYS C 370 " --> pdb=" O   ILE D 371 " (cutoff:3.500A)
      removed outlier: 7.744A  pdb=" N   THR D 373 " --> pdb=" O   LYS C 370 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   GLU C 372 " --> pdb=" O   THR D 373 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   LYS D 370 " --> pdb=" O   ILE F 371 " (cutoff:3.500A)
      removed outlier: 7.745A  pdb=" N   THR F 373 " --> pdb=" O   LYS D 370 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   GLU D 372 " --> pdb=" O   THR F 373 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'C' and resid 376 through 379
      removed outlier: 6.587A  pdb=" N   LEU C 376 " --> pdb=" O   THR D 377 " (cutoff:3.500A)
      removed outlier: 8.404A  pdb=" N   ARG D 379 " --> pdb=" O   LEU C 376 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   PHE C 378 " --> pdb=" O   ARG D 379 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   LEU D 376 " --> pdb=" O   THR F 377 " (cutoff:3.500A)
      removed outlier: 8.404A  pdb=" N   ARG F 379 " --> pdb=" O   LEU D 376 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   PHE D 378 " --> pdb=" O   ARG F 379 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7

    48 hydrogen bonds defined for protein.
    144 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.92

  Time building geometry restraints manager: 1.03 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 1003
        1.33 -     1.45: 864
        1.45 -     1.57: 2298
        1.57 -     1.69: 0
        1.69 -     1.81: 7
  Bond restraints: 4172
  Sorted by residual:
  bond pdb=" CG  HIS C 330 "
       pdb=" CD2 HIS C 330 "
    ideal  model  delta    sigma   weight residual
    1.354  1.314  0.040 1.10e-02 8.26e+03 1.35e+01
  bond pdb=" CG  HIS D 330 "
       pdb=" CD2 HIS D 330 "
    ideal  model  delta    sigma   weight residual
    1.354  1.314  0.040 1.10e-02 8.26e+03 1.34e+01
  bond pdb=" CG  HIS A 330 "
       pdb=" CD2 HIS A 330 "
    ideal  model  delta    sigma   weight residual
    1.354  1.314  0.040 1.10e-02 8.26e+03 1.33e+01
  bond pdb=" CG  HIS n 330 "
       pdb=" CD2 HIS n 330 "
    ideal  model  delta    sigma   weight residual
    1.354  1.314  0.040 1.10e-02 8.26e+03 1.32e+01
  bond pdb=" CG  HIS F 330 "
       pdb=" CD2 HIS F 330 "
    ideal  model  delta    sigma   weight residual
    1.354  1.314  0.040 1.10e-02 8.26e+03 1.32e+01
  ... (remaining 4167 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 4276
        1.91 -     3.81: 1083
        3.81 -     5.72: 190
        5.72 -     7.63: 23
        7.63 -     9.53: 7
  Bond angle restraints: 5579
  Sorted by residual:
  angle pdb=" N   PRO E 332 "
        pdb=" CA  PRO E 332 "
        pdb=" C   PRO E 332 "
      ideal   model   delta    sigma   weight residual
     110.55  120.08   -9.53 1.63e+00 3.76e-01 3.42e+01
  angle pdb=" N   PRO C 332 "
        pdb=" CA  PRO C 332 "
        pdb=" C   PRO C 332 "
      ideal   model   delta    sigma   weight residual
     110.55  120.06   -9.51 1.63e+00 3.76e-01 3.41e+01
  angle pdb=" N   PRO n 332 "
        pdb=" CA  PRO n 332 "
        pdb=" C   PRO n 332 "
      ideal   model   delta    sigma   weight residual
     110.55  120.06   -9.51 1.63e+00 3.76e-01 3.40e+01
  angle pdb=" N   PRO D 332 "
        pdb=" CA  PRO D 332 "
        pdb=" C   PRO D 332 "
      ideal   model   delta    sigma   weight residual
     110.55  120.06   -9.51 1.63e+00 3.76e-01 3.40e+01
  angle pdb=" N   PRO A 332 "
        pdb=" CA  PRO A 332 "
        pdb=" C   PRO A 332 "
      ideal   model   delta    sigma   weight residual
     110.55  120.05   -9.50 1.63e+00 3.76e-01 3.40e+01
  ... (remaining 5574 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.86: 2072
       10.86 -    21.72: 329
       21.72 -    32.58: 112
       32.58 -    43.43: 14
       43.43 -    54.29: 14
  Dihedral angle restraints: 2541
    sinusoidal: 1064
      harmonic: 1477
  Sorted by residual:
  dihedral pdb=" CA  GLY C 326 "
           pdb=" C   GLY C 326 "
           pdb=" N   ASN C 327 "
           pdb=" CA  ASN C 327 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.69  -29.31     0      5.00e+00 4.00e-02 3.44e+01
  dihedral pdb=" CA  GLY F 326 "
           pdb=" C   GLY F 326 "
           pdb=" N   ASN F 327 "
           pdb=" CA  ASN F 327 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.71  -29.29     0      5.00e+00 4.00e-02 3.43e+01
  dihedral pdb=" CA  GLY n 326 "
           pdb=" C   GLY n 326 "
           pdb=" N   ASN n 327 "
           pdb=" CA  ASN n 327 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.72  -29.28     0      5.00e+00 4.00e-02 3.43e+01
  ... (remaining 2538 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 217
       0.048 -    0.097: 194
       0.097 -    0.145: 121
       0.145 -    0.194: 70
       0.194 -    0.242: 21
  Chirality restraints: 623
  Sorted by residual:
  chirality pdb=" CA  LYS C 347 "
            pdb=" N   LYS C 347 "
            pdb=" C   LYS C 347 "
            pdb=" CB  LYS C 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CA  LYS A 347 "
            pdb=" N   LYS A 347 "
            pdb=" C   LYS A 347 "
            pdb=" CB  LYS A 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CA  LYS D 347 "
            pdb=" N   LYS D 347 "
            pdb=" C   LYS D 347 "
            pdb=" CB  LYS D 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.46e+00
  ... (remaining 620 not shown)

  Planarity restraints: 714
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG F 349 "    0.012 2.00e-02 2.50e+03   2.32e-02 5.40e+00
        pdb=" C   ARG F 349 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ARG F 349 "    0.015 2.00e-02 2.50e+03
        pdb=" N   VAL F 350 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 349 "    0.012 2.00e-02 2.50e+03   2.32e-02 5.37e+00
        pdb=" C   ARG B 349 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ARG B 349 "    0.015 2.00e-02 2.50e+03
        pdb=" N   VAL B 350 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG n 349 "    0.012 2.00e-02 2.50e+03   2.31e-02 5.35e+00
        pdb=" C   ARG n 349 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ARG n 349 "    0.015 2.00e-02 2.50e+03
        pdb=" N   VAL n 350 "    0.014 2.00e-02 2.50e+03
  ... (remaining 711 not shown)

  Histogram of nonbonded interaction distances:
        2.45 -     2.94: 1651
        2.94 -     3.43: 3616
        3.43 -     3.92: 5966
        3.92 -     4.41: 6465
        4.41 -     4.90: 13471
  Nonbonded interactions: 31169
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP E 314 "
            pdb=" OG  SER E 316 "
     model   vdw
     2.452 3.040
  nonbonded pdb=" OD1 ASP F 314 "
            pdb=" OG  SER F 316 "
     model   vdw
     2.453 3.040
  nonbonded pdb=" OD1 ASP n 314 "
            pdb=" OG  SER n 316 "
     model   vdw
     2.453 3.040
  nonbonded pdb=" OD1 ASP A 314 "
            pdb=" OG  SER A 316 "
     model   vdw
     2.453 3.040
  nonbonded pdb=" OD1 ASP B 314 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.453 3.040
  ... (remaining 31164 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'n'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.040
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.050   4172  Z= 0.608
  Angle     :  1.720   9.532   5579  Z= 1.106
  Chirality :  0.095   0.242    623
  Planarity :  0.010   0.052    714
  Dihedral  : 12.413  54.292   1603
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 0.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  1.49 %
    Favored  : 97.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.78 (0.24), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.87 (0.19), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.004   HIS B 330 
 PHE   0.008   0.003   PHE A 378 
 TYR   0.018   0.006   TYR B 310 
 ARG   0.005   0.002   ARG C 349 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: n  321 LYS cc_start: 0.8728 (mtpt) cc_final: 0.8321 (mttp)
REVERT: n  340 LYS cc_start: 0.9019 (mttt) cc_final: 0.8726 (mtpt)
REVERT: n  377 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8219 (p)
REVERT: A  321 LYS cc_start: 0.8869 (mtpt) cc_final: 0.8501 (mttm)
REVERT: A  340 LYS cc_start: 0.9140 (mttt) cc_final: 0.8846 (mtpp)
REVERT: B  311 LYS cc_start: 0.8875 (mttt) cc_final: 0.8510 (pttt)
REVERT: B  321 LYS cc_start: 0.8780 (mtpt) cc_final: 0.8369 (mttp)
REVERT: B  340 LYS cc_start: 0.9006 (mttt) cc_final: 0.8772 (mtpt)
REVERT: B  377 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8146 (p)
REVERT: C  321 LYS cc_start: 0.8896 (mtpt) cc_final: 0.8490 (mttp)
REVERT: C  340 LYS cc_start: 0.9053 (mttt) cc_final: 0.8824 (mtpt)
REVERT: C  377 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8523 (p)
REVERT: D  321 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8445 (mttp)
REVERT: D  340 LYS cc_start: 0.9093 (mttt) cc_final: 0.8777 (mtpt)
REVERT: D  349 ARG cc_start: 0.7655 (mtt-85) cc_final: 0.7432 (mtp180)
REVERT: E  321 LYS cc_start: 0.8661 (mtpt) cc_final: 0.8268 (mttp)
REVERT: E  340 LYS cc_start: 0.9062 (mttt) cc_final: 0.8720 (mtpt)
REVERT: E  349 ARG cc_start: 0.7717 (mtt-85) cc_final: 0.7461 (mtp180)
REVERT: E  371 ILE cc_start: 0.8732 (mm) cc_final: 0.8491 (mt)
REVERT: F  311 LYS cc_start: 0.8848 (mttt) cc_final: 0.8515 (pttt)
REVERT: F  321 LYS cc_start: 0.8773 (mtpt) cc_final: 0.8431 (mttm)
REVERT: F  331 LYS cc_start: 0.9074 (tttt) cc_final: 0.8823 (ttpt)
REVERT: F  340 LYS cc_start: 0.9064 (mttt) cc_final: 0.8712 (mtpt)
REVERT: F  349 ARG cc_start: 0.7744 (mtt-85) cc_final: 0.7502 (mtp180)
REVERT: F  377 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8461 (m)
  outliers start: 7
  outliers final: 0
  residues processed: 75
  average time/residue: 0.3044
  time to fit residues: 26.1265
Evaluate side-chains
  60 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain n residue  377 THR
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain C residue  377 THR
Chi-restraints excluded: chain F residue  377 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 37 optimal weight:   10.0000
   chunk 20 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   chunk 19 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 23 optimal weight:    9.9990
   chunk 28 optimal weight:    9.9990
   chunk 44 optimal weight:    5.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
n 351 GLN
n 362 HIS
A 330 HIS
A 351 GLN
A 362 HIS
B 351 GLN
B 362 HIS
C 330 HIS
C 351 GLN
C 362 HIS
D 351 GLN
D 362 HIS
E 351 GLN
E 362 HIS
F 351 GLN
F 362 HIS

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.126524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.101117 restraints weight = 5105.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3703 rms_B_bonded: 2.32
r_work: 0.3556 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3433 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   4172  Z= 0.296
  Angle     :  0.706   5.044   5579  Z= 0.377
  Chirality :  0.053   0.140    623
  Planarity :  0.003   0.025    714
  Dihedral  :  7.710  29.418    557
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  5.76 %
    Favored  : 93.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.14 (0.27), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.38 (0.21), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 362 
 PHE   0.006   0.002   PHE n 378 
 TYR   0.015   0.004   TYR B 310 
 ARG   0.003   0.000   ARG n 349 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.725 
Fit side-chains
REVERT: n  317 LYS cc_start: 0.8012 (ptmt) cc_final: 0.7671 (ptmm)
REVERT: n  340 LYS cc_start: 0.8791 (mttt) cc_final: 0.8347 (mtpt)
REVERT: A  340 LYS cc_start: 0.8953 (mttt) cc_final: 0.8500 (mtpt)
REVERT: B  311 LYS cc_start: 0.8407 (mttt) cc_final: 0.7970 (pttt)
REVERT: B  340 LYS cc_start: 0.8856 (mttt) cc_final: 0.8477 (mtpt)
REVERT: B  377 THR cc_start: 0.8221 (OUTLIER) cc_final: 0.8007 (p)
REVERT: C  340 LYS cc_start: 0.8764 (mttt) cc_final: 0.8399 (mtpt)
REVERT: D  340 LYS cc_start: 0.8894 (mttt) cc_final: 0.8407 (mtpt)
REVERT: D  369 LYS cc_start: 0.8733 (ptpt) cc_final: 0.8441 (ptpp)
REVERT: E  340 LYS cc_start: 0.8800 (mttt) cc_final: 0.8367 (mtpt)
REVERT: E  369 LYS cc_start: 0.8765 (ptpt) cc_final: 0.8405 (ptpp)
REVERT: F  311 LYS cc_start: 0.8495 (mttt) cc_final: 0.8100 (pttt)
REVERT: F  315 LEU cc_start: 0.8639 (mt) cc_final: 0.8179 (tt)
REVERT: F  331 LYS cc_start: 0.8674 (tttt) cc_final: 0.6939 (tptt)
REVERT: F  340 LYS cc_start: 0.8867 (mttt) cc_final: 0.8370 (mtpt)
REVERT: F  369 LYS cc_start: 0.8748 (ptpt) cc_final: 0.8413 (ptpp)
REVERT: F  377 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.8100 (p)
  outliers start: 4
  outliers final: 0
  residues processed: 59
  average time/residue: 0.3699
  time to fit residues: 24.8380
Evaluate side-chains
  54 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 52
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain F residue  377 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 5 optimal weight:    9.9990
   chunk 10 optimal weight:   10.0000
   chunk 4 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   chunk 6 optimal weight:   10.0000
   chunk 11 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   chunk 47 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 21 optimal weight:   10.0000
   overall best weight:    3.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.130302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.103532 restraints weight = 4904.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 2.32
r_work: 0.3584 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3463 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.2684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   4172  Z= 0.297
  Angle     :  0.644   6.176   5579  Z= 0.344
  Chirality :  0.052   0.132    623
  Planarity :  0.003   0.030    714
  Dihedral  :  6.922  31.101    555
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  :  6.82 %
    Favored  : 92.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.88 (0.27), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.19 (0.21), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 330 
 PHE   0.007   0.002   PHE B 378 
 TYR   0.016   0.004   TYR C 310 
 ARG   0.004   0.000   ARG B 349 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.404 
Fit side-chains
REVERT: n  315 LEU cc_start: 0.8554 (mt) cc_final: 0.8263 (tt)
REVERT: n  317 LYS cc_start: 0.8089 (ptmt) cc_final: 0.7761 (ptmm)
REVERT: n  340 LYS cc_start: 0.8800 (mttt) cc_final: 0.8360 (mtpt)
REVERT: B  311 LYS cc_start: 0.8361 (mttt) cc_final: 0.7941 (pttt)
REVERT: B  340 LYS cc_start: 0.8808 (mttt) cc_final: 0.8434 (mtpt)
REVERT: C  340 LYS cc_start: 0.8817 (mttt) cc_final: 0.8423 (mtpt)
REVERT: D  340 LYS cc_start: 0.8920 (mttt) cc_final: 0.8429 (mtpt)
REVERT: E  315 LEU cc_start: 0.8464 (mt) cc_final: 0.8162 (tt)
REVERT: E  340 LYS cc_start: 0.8817 (mttt) cc_final: 0.8362 (mtpt)
REVERT: E  369 LYS cc_start: 0.8767 (ptpt) cc_final: 0.8390 (ptpp)
REVERT: F  311 LYS cc_start: 0.8437 (mttt) cc_final: 0.8016 (pttt)
REVERT: F  315 LEU cc_start: 0.8445 (mt) cc_final: 0.8043 (tt)
REVERT: F  340 LYS cc_start: 0.8819 (mttt) cc_final: 0.8336 (mtpt)
  outliers start: 5
  outliers final: 0
  residues processed: 48
  average time/residue: 0.2655
  time to fit residues: 15.0834
Evaluate side-chains
  43 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 6 optimal weight:   10.0000
   chunk 36 optimal weight:    8.9990
   chunk 22 optimal weight:    7.9990
   chunk 18 optimal weight:   10.0000
   chunk 45 optimal weight:   10.0000
   chunk 40 optimal weight:    5.9990
   chunk 41 optimal weight:   20.0000
   chunk 39 optimal weight:    9.9990
   chunk 35 optimal weight:    7.9990
   chunk 44 optimal weight:    7.9990
   chunk 15 optimal weight:   20.0000
   overall best weight:    7.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 329 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.128085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.098937 restraints weight = 4893.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 2.57
r_work: 0.3418 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3282 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.2889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.046   4172  Z= 0.611
  Angle     :  0.804   5.807   5579  Z= 0.437
  Chirality :  0.057   0.155    623
  Planarity :  0.005   0.033    714
  Dihedral  :  7.316  21.226    553
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.14 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 11.94 %
    Favored  : 86.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.02 (0.27), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.29 (0.21), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS F 362 
 PHE   0.010   0.003   PHE B 378 
 TYR   0.025   0.006   TYR n 310 
 ARG   0.002   0.000   ARG B 349 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 0.523 
Fit side-chains
REVERT: n  340 LYS cc_start: 0.8827 (mttt) cc_final: 0.8318 (mtpt)
REVERT: B  311 LYS cc_start: 0.8397 (mttt) cc_final: 0.7889 (pttt)
REVERT: B  340 LYS cc_start: 0.8803 (mttt) cc_final: 0.8400 (mtpt)
REVERT: C  340 LYS cc_start: 0.8886 (mttt) cc_final: 0.8492 (mtpt)
REVERT: D  321 LYS cc_start: 0.8523 (mtpt) cc_final: 0.7979 (mttt)
REVERT: E  321 LYS cc_start: 0.8617 (mtpt) cc_final: 0.7994 (mttp)
REVERT: E  340 LYS cc_start: 0.8932 (mttt) cc_final: 0.8449 (mtpt)
REVERT: F  311 LYS cc_start: 0.8466 (mttt) cc_final: 0.7999 (pttt)
REVERT: F  315 LEU cc_start: 0.8565 (mt) cc_final: 0.8072 (tt)
REVERT: F  340 LYS cc_start: 0.8783 (mttt) cc_final: 0.8282 (mtpt)
  outliers start: 7
  outliers final: 3
  residues processed: 42
  average time/residue: 0.3185
  time to fit residues: 15.6974
Evaluate side-chains
  39 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain F residue  377 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 14 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0050
   chunk 0 optimal weight:    0.9990
   chunk 22 optimal weight:   10.0000
   chunk 8 optimal weight:    8.9990
   chunk 29 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    1.3998

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.138438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.111659 restraints weight = 5322.534|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 2.59
r_work: 0.3574 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3440 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.3337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   4172  Z= 0.146
  Angle     :  0.555   6.719   5579  Z= 0.288
  Chirality :  0.049   0.127    623
  Planarity :  0.003   0.031    714
  Dihedral  :  5.882  15.484    553
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 12.15 %
    Favored  : 86.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.61 (0.28), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.98 (0.21), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D 330 
 PHE   0.003   0.001   PHE B 378 
 TYR   0.008   0.002   TYR C 310 
 ARG   0.001   0.000   ARG E 379 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.460 
Fit side-chains
REVERT: n  340 LYS cc_start: 0.8712 (mttt) cc_final: 0.8261 (mtpt)
REVERT: B  311 LYS cc_start: 0.8212 (mttt) cc_final: 0.7732 (pttt)
REVERT: B  340 LYS cc_start: 0.8771 (mttt) cc_final: 0.8426 (mtpt)
REVERT: B  369 LYS cc_start: 0.8701 (ptpt) cc_final: 0.8461 (ptpp)
REVERT: C  340 LYS cc_start: 0.8828 (mttt) cc_final: 0.8426 (mtpt)
REVERT: D  344 LEU cc_start: 0.8616 (mp) cc_final: 0.8390 (mp)
REVERT: E  340 LYS cc_start: 0.8668 (mttt) cc_final: 0.8241 (mtpt)
REVERT: F  311 LYS cc_start: 0.8295 (mttt) cc_final: 0.7787 (pttt)
REVERT: F  315 LEU cc_start: 0.8465 (mt) cc_final: 0.8103 (tt)
REVERT: F  340 LYS cc_start: 0.8516 (mttt) cc_final: 0.8096 (mtpt)
  outliers start: 7
  outliers final: 2
  residues processed: 50
  average time/residue: 0.2119
  time to fit residues: 12.9900
Evaluate side-chains
  47 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 45
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain F residue  377 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 1 optimal weight:    5.9990
   chunk 28 optimal weight:   10.0000
   chunk 27 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 21 optimal weight:    9.9990
   chunk 44 optimal weight:    8.9990
   chunk 16 optimal weight:    6.9990
   chunk 43 optimal weight:   10.0000
   chunk 45 optimal weight:    0.0070
   overall best weight:    4.0006

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.133140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.104258 restraints weight = 4769.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 2.55
r_work: 0.3503 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3369 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.3296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   4172  Z= 0.331
  Angle     :  0.635   7.020   5579  Z= 0.332
  Chirality :  0.051   0.126    623
  Planarity :  0.003   0.028    714
  Dihedral  :  6.151  17.179    553
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 15.14 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.66 (0.28), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.02 (0.22), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 362 
 PHE   0.006   0.002   PHE B 378 
 TYR   0.015   0.004   TYR C 310 
 ARG   0.001   0.000   ARG B 349 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.947 
Fit side-chains
REVERT: n  340 LYS cc_start: 0.8713 (mttt) cc_final: 0.8231 (mtpt)
REVERT: B  311 LYS cc_start: 0.8245 (mttt) cc_final: 0.7746 (pttt)
REVERT: B  340 LYS cc_start: 0.8763 (mttt) cc_final: 0.8324 (mtpt)
REVERT: C  340 LYS cc_start: 0.8868 (mttt) cc_final: 0.8492 (mtpt)
REVERT: E  321 LYS cc_start: 0.8593 (mtpt) cc_final: 0.7963 (mttm)
REVERT: E  340 LYS cc_start: 0.8716 (mttt) cc_final: 0.8241 (mtpt)
REVERT: E  344 LEU cc_start: 0.9111 (mp) cc_final: 0.8713 (mp)
REVERT: F  311 LYS cc_start: 0.8356 (mttt) cc_final: 0.7846 (pttt)
REVERT: F  315 LEU cc_start: 0.8519 (mt) cc_final: 0.8125 (tt)
REVERT: F  340 LYS cc_start: 0.8660 (mttt) cc_final: 0.8118 (mtpt)
  outliers start: 5
  outliers final: 4
  residues processed: 42
  average time/residue: 0.3003
  time to fit residues: 15.8657
Evaluate side-chains
  43 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 39
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  377 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 30 optimal weight:    9.9990
   chunk 28 optimal weight:   20.0000
   chunk 38 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 5 optimal weight:    8.9990
   chunk 1 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0170
   chunk 12 optimal weight:    6.9990
   overall best weight:    3.2026

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.131146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.102676 restraints weight = 4880.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3663 rms_B_bonded: 2.61
r_work: 0.3516 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3380 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.3417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   4172  Z= 0.268
  Angle     :  0.593   6.452   5579  Z= 0.310
  Chirality :  0.050   0.124    623
  Planarity :  0.003   0.028    714
  Dihedral  :  5.963  16.886    553
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 14.50 %
    Favored  : 84.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.58 (0.28), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.96 (0.22), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D 330 
 PHE   0.005   0.001   PHE B 378 
 TYR   0.013   0.003   TYR C 310 
 ARG   0.001   0.000   ARG B 349 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.670 
Fit side-chains
REVERT: n  340 LYS cc_start: 0.8715 (mttt) cc_final: 0.8240 (mtpt)
REVERT: n  344 LEU cc_start: 0.8874 (mp) cc_final: 0.8648 (mp)
REVERT: A  344 LEU cc_start: 0.8630 (mp) cc_final: 0.8406 (mp)
REVERT: B  311 LYS cc_start: 0.8259 (mttt) cc_final: 0.7757 (pttt)
REVERT: B  340 LYS cc_start: 0.8793 (mttt) cc_final: 0.8403 (mtpt)
REVERT: C  340 LYS cc_start: 0.8875 (mttt) cc_final: 0.8507 (mtpt)
REVERT: E  321 LYS cc_start: 0.8620 (mtpt) cc_final: 0.8005 (mttm)
REVERT: E  340 LYS cc_start: 0.8665 (mttt) cc_final: 0.8202 (mtpt)
REVERT: E  344 LEU cc_start: 0.9143 (mp) cc_final: 0.8739 (mp)
REVERT: F  311 LYS cc_start: 0.8339 (mttt) cc_final: 0.7808 (pttt)
REVERT: F  315 LEU cc_start: 0.8515 (mt) cc_final: 0.8128 (tt)
REVERT: F  340 LYS cc_start: 0.8589 (mttt) cc_final: 0.8093 (mtpt)
  outliers start: 7
  outliers final: 5
  residues processed: 46
  average time/residue: 0.2659
  time to fit residues: 15.1138
Evaluate side-chains
  46 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 1.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain F residue  377 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 20 optimal weight:    8.9990
   chunk 26 optimal weight:    8.9990
   chunk 2 optimal weight:    4.9990
   chunk 7 optimal weight:   10.0000
   chunk 48 optimal weight:    0.6980
   chunk 1 optimal weight:    6.9990
   chunk 31 optimal weight:    7.9990
   chunk 15 optimal weight:    9.9990
   chunk 47 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   overall best weight:    4.3388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.129532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.102904 restraints weight = 4959.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3692 rms_B_bonded: 2.33
r_work: 0.3546 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3423 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.3430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   4172  Z= 0.360
  Angle     :  0.641   6.065   5579  Z= 0.338
  Chirality :  0.051   0.125    623
  Planarity :  0.003   0.027    714
  Dihedral  :  6.213  19.388    553
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 16.42 %
    Favored  : 81.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.72 (0.28), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.07 (0.21), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 362 
 PHE   0.007   0.002   PHE B 378 
 TYR   0.017   0.004   TYR C 310 
 ARG   0.001   0.000   ARG B 349 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 38
  time to evaluate  : 0.813 
Fit side-chains
REVERT: n  340 LYS cc_start: 0.8748 (mttt) cc_final: 0.8292 (mtpt)
REVERT: B  311 LYS cc_start: 0.8325 (mttt) cc_final: 0.7878 (pttt)
REVERT: B  340 LYS cc_start: 0.8776 (mttt) cc_final: 0.8382 (mtpt)
REVERT: C  340 LYS cc_start: 0.8891 (mttt) cc_final: 0.8540 (mtpt)
REVERT: D  321 LYS cc_start: 0.8620 (mtpt) cc_final: 0.8099 (mttt)
REVERT: E  321 LYS cc_start: 0.8664 (mtpt) cc_final: 0.8056 (mttm)
REVERT: E  340 LYS cc_start: 0.8713 (mttt) cc_final: 0.8251 (mtpt)
REVERT: F  311 LYS cc_start: 0.8414 (mttt) cc_final: 0.7971 (pttt)
REVERT: F  340 LYS cc_start: 0.8666 (mttt) cc_final: 0.8137 (mtpp)
  outliers start: 10
  outliers final: 8
  residues processed: 46
  average time/residue: 0.2762
  time to fit residues: 16.2090
Evaluate side-chains
  45 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 37
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  327 ASN
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  377 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 38 optimal weight:    0.0170
   chunk 10 optimal weight:   10.0000
   chunk 29 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 11 optimal weight:    6.9990
   chunk 21 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    3.4026

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.130679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.104170 restraints weight = 4948.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.3717 rms_B_bonded: 2.33
r_work: 0.3572 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3451 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.3548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   4172  Z= 0.282
  Angle     :  0.617   7.893   5579  Z= 0.319
  Chirality :  0.050   0.123    623
  Planarity :  0.003   0.025    714
  Dihedral  :  5.974  18.166    553
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 16.84 %
    Favored  : 81.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.64 (0.28), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.00 (0.22), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 362 
 PHE   0.005   0.001   PHE B 378 
 TYR   0.014   0.003   TYR C 310 
 ARG   0.001   0.000   ARG B 349 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.517 
Fit side-chains
REVERT: n  340 LYS cc_start: 0.8648 (mttt) cc_final: 0.8239 (mtpt)
REVERT: n  344 LEU cc_start: 0.8953 (mp) cc_final: 0.8737 (mp)
REVERT: B  311 LYS cc_start: 0.8315 (mttt) cc_final: 0.7875 (pttt)
REVERT: B  340 LYS cc_start: 0.8745 (mttt) cc_final: 0.8349 (mtpt)
REVERT: C  340 LYS cc_start: 0.8872 (mttt) cc_final: 0.8509 (mtpt)
REVERT: D  321 LYS cc_start: 0.8614 (mtpt) cc_final: 0.8101 (mttt)
REVERT: E  321 LYS cc_start: 0.8673 (mtpt) cc_final: 0.8065 (mttm)
REVERT: E  340 LYS cc_start: 0.8707 (mttt) cc_final: 0.8274 (mtpt)
REVERT: E  344 LEU cc_start: 0.9157 (mp) cc_final: 0.8779 (mp)
REVERT: F  311 LYS cc_start: 0.8371 (mttt) cc_final: 0.7931 (pttt)
REVERT: F  340 LYS cc_start: 0.8685 (mttt) cc_final: 0.8137 (mtpp)
  outliers start: 10
  outliers final: 8
  residues processed: 47
  average time/residue: 0.2269
  time to fit residues: 13.0626
Evaluate side-chains
  49 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  377 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 39 optimal weight:    6.9990
   chunk 45 optimal weight:    9.9990
   chunk 13 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 28 optimal weight:   10.0000
   chunk 26 optimal weight:    8.9990
   chunk 3 optimal weight:   10.0000
   chunk 19 optimal weight:    1.9990
   overall best weight:    4.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.128975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.102419 restraints weight = 4961.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 2.32
r_work: 0.3533 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3412 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.3554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   4172  Z= 0.373
  Angle     :  0.661   7.733   5579  Z= 0.345
  Chirality :  0.051   0.127    623
  Planarity :  0.003   0.023    714
  Dihedral  :  6.231  20.564    553
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 16.84 %
    Favored  : 81.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.75 (0.28), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.09 (0.21), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 362 
 PHE   0.007   0.002   PHE B 378 
 TYR   0.017   0.004   TYR A 310 
 ARG   0.001   0.000   ARG B 349 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.439 
Fit side-chains
REVERT: n  340 LYS cc_start: 0.8622 (mttt) cc_final: 0.8179 (mtpt)
REVERT: B  311 LYS cc_start: 0.8394 (mttt) cc_final: 0.7988 (pttt)
REVERT: B  340 LYS cc_start: 0.8730 (mttt) cc_final: 0.8329 (mtpt)
REVERT: C  340 LYS cc_start: 0.8880 (mttt) cc_final: 0.8514 (mtpt)
REVERT: D  321 LYS cc_start: 0.8631 (mtpt) cc_final: 0.8122 (mttt)
REVERT: D  340 LYS cc_start: 0.8732 (mttt) cc_final: 0.8311 (mtpt)
REVERT: E  321 LYS cc_start: 0.8675 (mtpt) cc_final: 0.8063 (mttm)
REVERT: E  340 LYS cc_start: 0.8718 (mttt) cc_final: 0.8270 (mtpt)
REVERT: E  344 LEU cc_start: 0.9139 (mp) cc_final: 0.8808 (mp)
REVERT: F  311 LYS cc_start: 0.8406 (mttt) cc_final: 0.7971 (pttt)
REVERT: F  340 LYS cc_start: 0.8697 (mttt) cc_final: 0.8145 (mtpp)
  outliers start: 10
  outliers final: 10
  residues processed: 48
  average time/residue: 0.3156
  time to fit residues: 18.2315
Evaluate side-chains
  49 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  327 ASN
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain E residue  357 LEU
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  377 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 45 optimal weight:    4.9990
   chunk 8 optimal weight:    5.9990
   chunk 3 optimal weight:    9.9990
   chunk 10 optimal weight:    8.9990
   chunk 35 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   overall best weight:    3.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.129092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.102461 restraints weight = 4927.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 2.37
r_work: 0.3548 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3424 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.3641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   4172  Z= 0.311
  Angle     :  0.626   7.667   5579  Z= 0.327
  Chirality :  0.050   0.125    623
  Planarity :  0.003   0.024    714
  Dihedral  :  6.047  19.515    553
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 16.84 %
    Favored  : 81.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.71 (0.28), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.06 (0.21), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 362 
 PHE   0.006   0.002   PHE B 378 
 TYR   0.015   0.004   TYR A 310 
 ARG   0.001   0.000   ARG B 349 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2571.29 seconds
wall clock time: 47 minutes 11.91 seconds (2831.91 seconds total)